Abstract 625: Immunophenotyping of TCR and BCR clonotypes

TCR and BCR repertoire profiling holds great potential for understanding disease mechanisms and for development of new therapeutics in infectious diseases, autoimmunity and in immuno-oncology. However, this potential could be greatly improved by combining information about receptor clonotypes with immunophenotypes of T and B cells. To facilitate these studies, we developed a novel technology for combined profiling of all human TCR and BCR variable regions and phenotypic characterization of immune cells. The developed TCR/BCR immunophenotyping method involves multiplex RT-PCR amplification and sequencing of CDR3 regions of TCR and BCR genes and a set of the most informative T- and B-cell phenotyping genes. Bioinformatic analysis of NGS data allows profiling of TCR/BCR clonotypes, and identification of major immune cell subtypes and their activation status. Data will be presented showing how combined TCR/BCR clonotype analysis combined with targeted expression profiling of immune cells can be applied for large-scale discovery of novel cell typing and activation biomarkers in several immune-responsive model systems. Preliminary studies indicate the assay has unparalleled throughput, sensitivity, and improved cost-effectiveness for high-throughput immunity biomarker discovery applications.

Citation Format: Alex Chenchik, Mikhail Makhanov, Tianbing Liu, Lester Kobzik. Immunophenotyping of TCR and BCR clonotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 625.

Abstract 5868: Cell barcoding, genetic screens and expression profiling at a single-cell level

Novel single-cell methods for profiling clonal composition and phenotypes of genetically modified cancer cells may improve understanding of tumorigenesis and guide the development of new anti-cancer drugs. To facilitate these studies, we developed a panel of lentiviral barcoded sgRNA libraries to label and monitor cancer cells in time-course experiments in vitro and in mouse xenograft models. The sgRNA effectors and cellular barcodes are transcribed from lentiviral constructs and can be detected by NGS in a single-cell RNA expression profiling assay, allowing characterization of the subpopulation of cells descended from a single, barcoded knockout progenitor cell. To scale up genetic analysis, cell barcodes were incorporated in conjunction with sgRNA effector libraries to identify clonal phenotypic changes induced by specific genetic disruptions in progeny cells derived from a single progenitor cell. However, effective single-cell genetic screening designed for even only a few hundred genes requires expression profiling of one hundred thousand cells (or more) and is not practical using currently available instrumentation. Data will be presented showing how genetic screen technology combined with targeted RNA expression profiling of barcoded knockout cells can be applied for large-scale genetic screens and significantly improve phenotyping of distinct cell populations in several cancer model systems. Preliminary studies demonstrate the assay to have unparalleled throughput, sensitivity, and improved cost-effectiveness for high-throughput drug target discovery applications.

Citation Format: Alex Chenchik, Mikhail Makhanov, Russell Darst, Debbie Deng, Donato Tedesco, Paul Diehl, Lester Kobzik. Cell barcoding, genetic screens and expression profiling at a single-cell level [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5868.

Abstract 3426: Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis

Pooled lentiviral libraries of CRISPR sgRNAs to mediate genome-wide gene knockout have become an invaluable tool for uncovering the functional genetic drivers required for a biological response. Another type of pooled lentiviral library designed with unique DNA sequence tags have also been used to label large populations of cells with unique cell-specific barcodes which allows monitoring changes in sub-populations of cells with distinct phenotypes over time. We have combined cell barcodes with CRISPR sgRNA to construct libraries that enable the identification of multiple occurrences of a common phenotypic response from independent transductions of the same sgRNA effector. Specifically, we demonstrate how this sort of library can be used to identify genes whose activation promotes metastasis of tumors derived from MDA-MB-231 cells engrafted into mice after transduction with a barcoded CRISPR-activation (CRISPRa) sgRNA library. By incorporating multiple barcodes with each sgRNA effector, it is possible to see that, not only are cells in metastatic tumors more likely to have a particular sgRNA targeted to a certain gene, but also that independent transductions of that sgRNA sequence lead to multiple independent metastatic events. With multiple independent clones producing the same phenotype, it is possible to confidently isolate the sgRNA, and by implication, the increased activation of its gene target, as the primary cause of the metastatic phenotype.

Citation Format: Alex Chenchik, Paul Diehl, Mikhail Makhanov. Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3426.

Abstract A059: Targeted RNA expression profiling for biomarker discovery in complex biologic samples

New rapid and robust transcriptome-based methods for cellular characterization of the tumor microenvironment and biomarker discovery are required to improve prognosis and treatment of cancer and other diseases. However, challenges with current approaches for the above applications include high sample requirements, poor sensitivity, low dynamic range, and limited throughput. To address these limitations, we have developed the DriverMap targeted RNA expression profiling assay using a genome-wide set of 19,000 validated primer pairs that leverages the sensitivity of multiplex RT-PCR with the throughput and digital readout depth of next-generation sequencing (NGS). Starting from just 10pg (single-cell) to 100ng (10,000 cells) of total RNA is sufficient to quantify over 5 orders of magnitude variation in gene expression levels with performance similar to conventional qRT-PCR. Further, the use of gene-specific primers enables direct analysis of total RNA isolate and obviates the need for globin and rRNA depletion from whole blood samples. In this study, we present the performance of the assay for immunophenotyping of immune cells in whole blood samples from sepsis patients and assess the immune responses to complex immunomodulatory stimuli in an ex vivo model system. We will also present profiling results that demonstrate how this assay can be used to analyze the level of immune cell infiltration in tumor samples, and identify active pathways in tumor and xenograft samples. Preliminary studies demonstrate the assay’s unparalleled specificity and sensitivity, resulting in better detection of low-abundance mRNA transcripts as well as an improved cost-effectiveness for high-throughput clinical applications.

Citation Format: Alex Chenchik, Costa Frangou, Mikhail Makhanov. Targeted RNA expression profiling for biomarker discovery in complex biologic samples [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A059.

Abstract 744: Cancer immunotherapy biomarker profiling assay

Selecting patients predisposed to respond to existing and novel immunotherapy treatments requires the development of novel prognostic and predictive biomarkers. Recent reports have identified several gene expression signatures specific for immunity status and immune contexture in solid tumor microenvironments, and these enable predictions of efficacy of a number of chemo- and immunotherapeutics. Robust methods for molecular characterizations of the immune mechanism in the tumor microenvironment are essential to meet the imminent need for diagnostic approaches that identify patient populations responsive to the growing number of immunotherapeutic treatments. Toward this goal, we developed the Cancer ImmuneNet 2500 (CIN2500) assay for profiling cellular composition in the tumor microenvironment and discovery of novel prognostic and predictive immune response biomarkers.

The CIN2500 panel provides signatures for approximately 400 immunity-related genes from 16 predictive and prognostic core genes that have been validated in recent chemo- and immunotherapy clinical trials across several tumor types, including melanoma, colorectal, breast, and lung cancers. In addition, using computational analysis of an immunotherapy network model, we predicted and included in the assay approximately 300 key nodes in pathways specific for antigen presentation and recognition, inhibition, activation and motility of immune cells, and adhesion and apoptosis of cancer cells. The CIN2500 panel also includes a comprehensive set of 1,700 genes specific for detection and quantitative profiling in the tumor microenvironment of different types of activated immune cells of adaptive and innate immunity, and stromal, fibroblast, cancer, endothelial and adipose cell types.

The CIN2500 assay quantitatively profiles the expression levels of approximately 2,500 key cancer genes from 10-100ng of total RNA using multiplex RT-PCR amplification followed by Next-Generation Sequencing (NGS). Built-in standards for each gene target enable sample-to-sample calibration of the NGS data and provide a reference to adjust for background noise that often depends on the quality of samples. Control studies have shown that the CIN2500 assay quantifiably measures 4 orders of magnitude variation in the expression levels of 2,500 immune-related genes from as few as 100 cells in whole lysate, and profiles from frozen biopsies, surgically-removed tumor samples, PBMCs, and FFPE clinical samples show a comparable range and sensitivity. We will present profiling data from infiltrating immune cells and key intact and deficient immune mechanisms in the tumor microenvironment of breast cancer samples to demonstrate the performance and utility of the CIN2500 assay.

Citation Format: Alex Chenchik, Leonid Iakoubov, Mikhail Makhanov, Costa Frangou. Cancer immunotherapy biomarker profiling assay. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 744.

Abstract 4354: CRISPR/Cas9 genome-wide gRNA library for target identification

Genome-wide loss-of-function screening is a fundamental method to identify genes responsible for driving biological responses, and complex pooled lentiviral-based libraries expressing large numbers of genetic disruptors, such as shRNAs, make large-scale cell screening practical. While RNAi-based approaches have proven to be an effective strategy for these screens, recent work suggests CRISPR technology offers an effective alternative. Although shRNA and sgRNA pooled library screens are similar in concept, the gene interruption with the two techniques occurs by a very different mechanism so some divergence may be expected when comparing results obtained using one method versus the other.

To investigate the potential difference in the two methodologies, we performed parallel dropout viability screens to identify essential genes in a pair of primary isogenic CML cell lines using a CRISPR/Cas9 knockout library and an RNA interference (RNAi) library targeting the same set of 6,300 genes with the same number of targeted effectors (sgRNA or shRNA) for each gene. The results showed significant, but not complete, overlap in the essential genes identified by each assay in each cell line indicating that both approaches are effective to identify the majority of essential genes in a cell system. However, analysis did indicate that a small number of essential targets were only identified with CRISPR and certain unique targets seemed to show up only in the RNAi screen results. By combining data from the two screening methodologies, a consistent number of viability genes and pathways could be identified and subsequently validated by independent cell based assays at a very high confirmation rate.

Citation Format: Donato Tedesco, Paul Diehl, Mikhail Makhanov, Sylvain Baron, Dmitry Suchkov, Costa Frangou, Alex Chenchik. CRISPR/Cas9 genome-wide gRNA library for target identification. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4354.

CancerNet: Molecular profiling of tumor microenvironment for biomarker discovery

Human carcinomas consist of a complex mixture of neoplastic epithelial cells, endothelial cells, fibroblasts, myofibroblasts, and immune cells, which collectively form the tumor stroma. These cells are implicated in disease progression, metastasis and drug resistance. The clinical importance of tumor immune infiltrates has been an emerging area in triple negative breast cancer (TNBC) research where increased immune infiltrate predicts both response to chemotherapy and improved survival. Quantitative molecular profiles of tumor-associated normal cells may provide important insights into tumor biology and facilitate the discovery of new biomarkers and therapeutic targets. To this end, we have developed CancerNet, a comprehensive targeted RNA-Seq cancer immuno-panel that profiles ~2,000 genes and distinguishes 37 human hematopoietic cell phenotypes, (including naïve and memory B cells, seven T-cell types, dendritic cells, plasma cells, natural killer (NK) cells and myeloid subsets), genes involved in checkpoint blockade and immunotherapy biomarkers, immune cell activation and canonical immune pathway genes for both innate adaptive and humoral immune responses. In this study, we present an assay that characterizes the cellular composition of the immune/stromal/cancer cell tumor microenvironment and determines the activation status of infiltrating immune cells in primary tumor tissues from TNBC patients. Preliminary studies demonstrate the assay’s unparalleled specificity and sensitivity resulting in better detection of low abundance mRNA transcripts as well as an improved cost-effectiveness for high-throughput clinical Next-Gen applications.

Abstract C161: CRISPR/Cas9 genome-wide gRNA library screening platform

CRISPR/Cas9 gene knock-out technology can be used as a powerful tool for large-scale functional genomic analysis in mammalian cells. With the goal to establish a cost-effective functional genomics platform for the discovery of therapeutic targets, we developed a highly functional high throughput lentiviral gRNA/CRISPR screening platform, enabling scientists to perform pooled format genome-wide CRISPR/Cas9 genetic screens. Three 55K gRNA libraries were designed to cover the whole protein-encoding human genome with a redundancy of 8 gRNAs per gene. As supporting tools, we developed protocols, reagents, and software tools for hit validation and target prioritization.

Here we show the results of parallel genetic screens in a pair of isogenic CML cell lines (CML-R and CML-P), where the performance of CRISPR/Cas9 and RNAi screening platforms was compared for each cell line.

Citation Format: Donato Tedesco, Paul Diehl, Mikhail Makhanov, Sylvain Baron, Dmitry Suchkov, Alex Chenchik. CRISPR/Cas9 genome-wide gRNA library screening platform. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C161.

Abstract 3384: Cancer Core 125 Panel for quantitative expression and mutation profiling

Molecular profiling of heterogeneous circulating tumor cells (CTCs) and tumor biopsy samples at the single-cell level is critical for identifying different cancer cell subpopulations and understanding their value in predicting metastatic cancer progression and responses to treatment. Unfortunately, the isolation and comprehensive characterization of hundreds to thousands of individual cancer cells present formidable analytical and technical challenges.

To this end, we developed a high-throughput (HT) HiCellex technology to obtain the genome-wide expression and mutation profiles of hundreds to thousands of epithelial cancer cells at the single cell level. Importantly, HiCellex allows selective molecular profiling of a complete set of viable cells at the single-cell level in the presence of contaminating leukocytes without physical separation of individual cells. The genetic profiling technology uses unique cell-specific molecular barcodes to label mRNAs in individual viable cancer cells by a spliceosome-mediated trans-splicing mechanism. Barcoded trans-splicing constructs, necessary for the labeling of the entire population of pre-mRNAs, are delivered and expressed in a pool of target cancer cells with lentiviral vectors. Digital expression data are generated by HT sequencing of barcoded amplified cDNAs and easily cluster to each cell in silico using cell-specific barcodes.

This presentation will provide results of development and validation of genome-wide and multiplex RT-PCR profiling assay of the 500 most informative subtyping and metastatic signature genes (MGS) in model cancer cell lines, CTC and tumor samples. The developed HiCellex 500 MGS profiling assay is a cost-effective approach to effectively characterize, subtype and identify prognostic and diagnostic biomarkers in heterogeneous cancer cells at the single-cell level.

Citation Format: Alex Chenchik, Mikhail Makhanov, Gregory Dolganov, Stefanie Jeffrey. Cancer Core 125 Panel for quantitative expression and mutation profiling. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3384. doi:10.1158/1538-7445.AM2015-3384

Abstract 1112: Loss-of-function genetic screening with shRNA and CRISPR libraries

Genome-wide loss-of-function screens provide a direct approach to identify the genes regulating biological responses and find new therapeutic targets. While RNAi screens have proven an effective tool for these screens, CRISPR/CAS9 provides an alternative approach to implement these screens. To complement our established shRNA screening platform, we have developed pooled format genome-wide modular sgRNA libraries for cost-effective functional CRISPR knockout screens. Pooled sgRNA and shRNA libraries were then run to identify lethal interactions in isogenic PDX-derived cell line pairs.

Citation Format: Donato Tedesco, Mikhail Makhanov, Sylvain Baron, Dmitry Suchkov, Alex Chenchik. Loss-of-function genetic screening with shRNA and CRISPR libraries. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1112. doi:10.1158/1538-7445.AM2015-1112

Abstract 1721: Moving beyond in vitro models and addressing the challenges of pooled RNAi screens in mouse xenografts

RNAi loss-of-function screening with pooled shRNA expression libraries has proven to be a useful tool to identify essential cancer genes and drug resistance mechanisms in numerous cell lines in vitro. The effects of knocking down large numbers of genes on cancer cell growth and viability can be measured simultaneously using this approach. Now there is considerable interest to adapt RNAi viability screens to ex vivo xenograft mouse models. However, small take rates, growth rate variance of cells, and differing cell microenvironments in these more complex tumor models impose significant challenges to this sort of assay. We have developed a novel approach based on the use of pooled shRNA libraries with clonal barcodes that enables proliferation measurements of clonal populations produced by the individual shRNA-expressing founder cells that produce the tumor. This RNAi clonal analysis provides a basis to separate, across large cell populations, the external parameters that strongly influence cell growth rates from shRNA-induced growth inhibition in these systems. We will present in vivo RNAi screening validation data for several cancer models.

Citation Format: Paul Diehl, Donato Tedesco, Kyle Bonneau, Mikhail Makhanov, Debbie Deng, Peiqing Sun, Alex Chenchik. Moving beyond in vitro models and addressing the challenges of pooled RNAi screens in mouse xenografts. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1721. doi:10.1158/1538-7445.AM2015-1721

Abstract A12: Viability screens in leukemic and breast cancer cells with pooled lentiviral shRNA libraries identify potential therapeutic targets and synthetic or synergistic lethal interactions

One strategy to circumvent problems with conventional chemotherapy is to develop drugs against more specific cancer targets. Another is to use molecularly targeted agent (MTA) combinations to circumvent tumor resistance and increase the therapeutic index. Such synergistically lethal (SL) MTA combinations, however, are not easily predicted based on our rudimentary knowledge of cancer biology and drug action mechanisms.

In the first strategy, our aim was to identify genes modulating proliferation and survival in leukemic cell lines (K562, Jurkat, and Raji) using a pooled lentiviral library expressing 27,500 shRNA targeting 5,043 human pathway-associated genes. Cells were transduced by the viral library and collected at several time points. Bar-codes were amplified from genomic DNA and sequenced (Illumina GAIIx). In the second strategy, we have adapted the same approach to combinatorially screen shRNA sequences targeting 40 DNA Damage and Repair (DDR) genes to discover additive and synergistic combinations that generate a synthetic-lethal phenotype. Human mammary epithelial cancer (HMEC) cells were transduced with a 27K shRNA SL DDR lentiviral library comprised of a redundant set of 16 binary shRNA constructs for each possible gene-gene combination (1,600). The library-transduced HMEC cells were grown for ten days, then bar-codes amplified and sequenced (Illumina HiSeq2000).

The viability screen with leukemic cell lines identified more than 250 essential genes for each panel of cells. Subsequent validation using single shRNA-expressing constructs showed that in each screen, about 80% of shRNAs identified did indeed lead to cell death when transduced in cells. Analysis of the identified essential genes for known biological interactions revealed several non-random clusters of interacting proteins that provide some insight into signaling pathways and protein networks specific to these cancers. The SL screen in HMEC cells identified 10 SL shRNA pair candidates including known SL shRNA pair PARP1/BRCA1. Additional analysis of lethal combinations indicated redundant, complementary, and compensatory responses in cancer cells.

We believe that newly discovered hematopoietic-specific genes represent potentially novel drug targets. Moreover, they can be used to develop and establish both novel cancer targeted therapies and myeloablative conditioning regimens with decreased toxicity. Based on SL screen results in HMEC cells, we believe that comprehensive experimental annotation of SL gene-gene interactions in a wider range of cancer and normal cells will not only predict the most promising synergistic lethal combinations but also allow the development of a new generation of multi-specific, highly effective anti-cancer therapeutics with unique mechanisms of action.

Citation Format: Donato Tedesco, Kyle Bonneau, Mikhail Makhanov, Debbie Deng, Karim Hyder, Paul Diehl, Costas G. Frangou, Alex Chenchik. Viability screens in leukemic and breast cancer cells with pooled lentiviral shRNA libraries identify potential therapeutic targets and synthetic or synergistic lethal interactions. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A12.

Abstract 3160: Open-source RNAi genetic screen platform: discovery of drug targets in cancer cell models

We have developed an open-source RNAi genetic screening technology, funded in part by NIH grants and freely available to the scientific community. This platform can be used for functional discovery of drug targets associated with viability and regulation of signaling pathways in cancer cells. Here we present a novel, free public resource for genome-wide RNAi screens: DECIPHER pooled lentiviral shRNA libraries. Results are shown from two RNAi screens with DECIPHER shRNA libraries: one “drop-out” screen to identify genes essential for viability in a panel of leukemic cells, and a second “rescue” screen to identify genes required for FAS induced apoptosis. Both screens found a combination of known and novel signaling pathway and regulatory genes whose functions were confirmed to be required to produce the biological responses. From the viability screens in the panel of leukemia cell lines, subsequent validation using single shRNA-expressing constructs showed that about 80% of the shRNAs identified in each complex library screen did in fact lead to cell death when transduced in cells. Analysis of the identified essential genes for known biological interactions revealed non-random clusters of interacting proteins that provide a useful strategy for prioritization of potential targets. Analysis of the lethal combinations indicates redundant, complementary, and compensatory responses in cancer cells. In the case of the FAS-induced apoptosis, in vitro screening data also enabled us to select targets that protected mice from FAS-induced hepatic failure. These results demonstrate that complex pooled shRNA libraries provide a highly efficient, flexible, and cost-effective alternative to array-based RNAi screening methods for identifying genes regulating biological responses and possible new therapeutic targets.

Citation Format: Andrei Komarov, Mikhail Makhanov, Elena Komarova, Lilya Novototzkaja, Michael Yeluashvili, Dmitry Suchkov, Kyle Bonneau, Donato Tedesco, Costa G. Frangou, Paul Diehl, Debbie Deng, Karim Hyder, Pavel Komarov, Andrei Gudkov, Alex Chenchik. Open-source RNAi genetic screen platform: discovery of drug targets in cancer cell models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3160. doi:10.1158/1538-7445.AM2013-3160

Abstract 3172: Pooled RNAi screens in xenograft mouse models

We present results of clonal analysis studies aimed at characterizing the heterogeneity of in vivo cancer cell growth in xenograft models. Using a high-throughput sequencing method, we followed the fate of thousands of individually bar-coded cancer cells grown in vitro, or in vivo upon sub-cutaneous implantation in immunocompromised mice. By precisely and reproducibly quantifying clonal cancer cell growth in vivo, we found that xenograft growth is marked by a phenomenon of clonal dominance, in which a small subset of cancer cell sub-clones account for the bulk of the resulting tumor mass. This phenomenon has important implications for the field of in vivo shRNA screening. Subsequently, we developed a new proprietary clonal RNAi screening platform specifically designed to circumscribe the clonal dominance effect in xenograft model viability screens. We used this technology to perform xenograft “drop-out” screens in a panel of tumorigenic cell lines, including human breast, ovarian and colon carcinomas. Preliminary data will be presented. These results demonstrate that complex pooled shRNA libraries provide a highly efficient, flexible, and unique tool for in vivo screens aimed the discovery of potential cancer therapy targets.

Citation Format: Donato Tedesco, Kyle Bonneau, Mikhail Makhanov, Debbie Deng, Paul Diehl, Peiqing Sun, Alex Chenchik. Pooled RNAi screens in xenograft mouse models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3172. doi:10.1158/1538-7445.AM2013-3172

Abstract 876: Viability screens in leukemic and breast cancer cells with pooled lentiviral shRNA libraries identify potential therapeutic targets and synergistic lethal interactions

Background: One strategy to circumvent problems with conventional chemotherapy is to develop drugs against more specific cancer targets. Another is to use molecularly targeted agent (MTA) combinations to circumvent tumor resistance and increase the therapeutic index. Such synergistically lethal (SL) MTA combinations, however, are not easily predicted based on our rudimentary knowledge of cancer biology and drug action mechanisms. Method: In the first strategy, our aim was to identify genes modulating proliferation and survival in leukemic cell lines (K562, Jurkat, and Raji) using a pooled lentiviral library expressing 27,500 shRNA targeting 5,043 human pathway-associated genes. Cells were transduced by the viral library and collected at several time points. Bar-codes were amplified from genomic DNA and sequenced (Illumina GAIIx). In the second strategy, we have adapted the same approach to combinatorially screen shRNA sequences targeting 40 DNA Damage and Repair (DDR) genes to discover additive and synergistic combinations that generate a synthetic-lethal phenotype. Human mammary epithelial cancer (HMEC) cells were transduced with a 27K shRNA SL DDR lentiviral library comprised of a redundant set of 16 binary shRNA constructs for each possible gene-gene combination (1,600). The library-transduced HMEC cells were grown for ten days, then bar-codes amplified and sequenced (Illumina HiSeq2000). Results: The viability screen with leukemic cell lines identified more than 250 essential genes for each panel of cells. Subsequent validation using single shRNA-expressing constructs showed that in each screen, about 80% of shRNAs identified did indeed lead to cell death when transduced in cells. Analysis of the identified essential genes for known biological interactions revealed several non-random clusters of interacting proteins that provide some insight into signaling pathways and protein networks specific to these cancers. The SL screen in HMEC cells identified 10 SL shRNA pair candidates including known SL shRNA pair PARP1/BRCA1. Additional analysis of lethal combinations indicated redundant, complementary, and compensatory responses in cancer cells. Conclusion: We believe that newly discovered hematopoietic-specific genes represent potentially novel drug targets. Moreover, they can be used to develop and establish both novel cancer targeted therapies and myeloablative conditioning regimens with decreased toxicity. Based on SL screen results in HMEC cells, we believe that comprehensive experimental annotation of SL gene-gene interactions in a wider range of cancer and normal cells will not only predict the most promising synergistic lethal combinations but also allow the development of a new generation of multi-specific, highly effective anti-cancer therapeutics with unique mechanisms of action.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 876. doi:1538-7445.AM2012-876

Abstract C159: Identification of potential cancer drug targets using HT RNAi screening with pooled shRNA libraries

Genes modulating proliferation and survival in oncogenic cells have been identified using pooled lentiviral-based libraries expressing many thousands of shRNAs. Viability assays with human isogenic mammary epithelial cells (HMEC) and blood cancer cell lines transduced with these shRNA libraries targeting thousands of genes identified hundreds of essential genes for each panel of cells. Subsequent validation using single shRNA-expressing constructs showed that about 80% of the shRNAs identified in each complex library screen did in fact lead to cell death when transduced in cells. Analysis of the identified essential genes for known biological interactions revealed non-random clusters of interacting proteins that provide some insight into signaling pathways and protein networks specific to these cancers. Also, we have recently adapted the approach to combinatorially screen shRNA sequences targeting hundreds of genes to discover additive and synergistic combinations that generate a synthetic-lethal phenotype. Analysis of the lethal combinations indicates redundant, complementary, and compensatory responses in cancer cells. This presentation will provide an overview of the screening platform, our approach to shRNA library design, and results from the screens for cancer cell-specific lethal and synthetic-lethal genes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C159.

Abstract A36: Viability screens in leukemic and breast cancer cells with pooled lentiviral shRNA libraries identify potential therapeutic targets and synergistic lethal interactions

Background: One strategy to circumvent problems with conventional chemotherapy is to develop drugs against more specific cancer targets. Another is to use molecularly targeted agent (MTA) combinations to circumvent tumor resistance and increase the therapeutic index. Such synergistically lethal (SL) MTA combinations, however, are not easily predicted based on our rudimentary knowledge of cancer biology and drug action mechanisms.

Method: In the first strategy, our aim was to identify genes modulating proliferation and survival in leukemic cell lines (K562, Jurkat, and Raji) using a pooled lentiviral-based library expressing 27,500 shRNA targeting 5,043 human pathway-associated genes. Cells were transduced by the viral library, selected using puromycin, and collected at several time points. Genomic DNA was extracted from cell populations, and shRNA/bar-codes PCR amplified and subjected to HT sequencing (lllumina GAIIx). In the second strategy, we have adapted the same approach to combinatorially screen shRNA sequences targeting 40 rationally selected DNA Damage and Repair (DDR) genes to discover additive and synergistic combinations that generate a synthetic-lethal phenotype. Human mammary epithelial cancer (HMEC) cells were tranduced with a 27,000 (27K) shRNA SL DDR lentiviral library comprised of a redundant set of 16 binary shRNA constructs for each possible gene-gene combination (1,600). The library-transduced HMEC cells were grown for three days in the presence of puromycin to select for infected cells and then grown for one week (without puromycin). Genomic DNA was extracted from cell populations, and bar-codes were PCR amplified and subjected to HT sequencing (Illumina HiSeq 2000).

Results: The viability screen with leukemic cell lines identified more than 250 essential genes for each panel of cells. Subsequent validation using single shRNA-expressing constructs showed that in each screen, about 80% of shRNAs identified did indeed lead to cell death when transduced in cells. Analysis of the identified essential genes for known biological interactions revealed several non-random clusters of interacting proteins that provide some insight into signaling pathways and protein networks specific to these cancers. The SL screen in HMEC cells identified approximately 10 SL shRNA pair candidates including known SL shRNA pair PARP1/BRCA1. Additional analysis of lethal combinations indicated redundant, complementary, and compensatory responses in cancer cells.

Conclusion: We believe that newly discovered hematopoietic-specific genes represent potentially novel drug targets. Moreover, they can be used to develop and establish both novel cancer targeted therapies and myeloablative conditioning regimens with decreased toxicity. Based on SL screen results in HMEC cells, we believe that comprehensive experimental annotation of SL gene-gene interactions in a wider range of cancer and normal cells will not only predict the most promising synergistic lethal combinations but also allow the development of a new generation of multispecific, highly effective anticancer therapeutics with unique mechanisms of action.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A36.

Optimization of a Genome-Wide Disordered Lentivector-Based Short Hairpin RNA Library

To obtain a whole genome library that suppresses the total diversity of human mRNAs, lentiviral vector constructs and a short hairpin RNA (shRNA) expression cassette were optimized. The optimization of the vector increased the virus titer in preparations by 15-20 times. A simple shRNA structure with a 21-bp stem proved to be the most effective. Lentivector-based shRNA expression constructs were obtained by using puro(R), copGFP, or H-2K(k) as a selectable marker. The efficiency of the optimized library was demonstrated when screening for shRNAs reactivating the tumor suppressor p53 in HeLa cells. Cells carried a reporter construct ensuring p53-responsive synthesis of a fluorescent protein, which allowed selection of cells with reactivated p53 by flow cytometry.

[Genome-wide lentivector-based pooled shRNA library optimization]

We have optimized lentiviral vector constructs and cassettes for expression of short hairpin RNAs (shRNAs) in order to create genome-wide library capable of inhibition of full variety of human mRNAs. The vector optimization has resulted in 15-20-fold improvement in virus stock titers. We found that in the context of lentiviral vector the most effective structure for the shRNA is simple hairpin with 21 nucleotide stem. The shRNA-expressing lentiviral constructs contain choice of puro(R), copGFP or H-2K(k) selective markers. The efficiency of the optimized library was evaluated in experiments on screening of shRNAs that reactivate oncosuppressor p53 in HeLa cells. The cells contained reporter construct with p53-dependent expression of a fluorescent protein, which allows cytofluorimetric isolation of cell population with reactivated p53.